PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Vradi0185s00050.1

Organism

Vigna radiata

Taxonomic ID

157791

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna

Family

ARF

Protein Properties

Length: 876aa MW: 97419.3 Da PI: 6.7372

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Vradi0185s00050.1	genome	SNU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	74.7	1e-23	124	225	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 f+k+lt sd++++g +++ +++a+e+ + k++ +++l +d++g++W++k+i+r++++r++l++GW+ Fv++++L +gD ++F + Vradi0185s00050.1 124 FCKTLTASDTSTHGGFSVLRRHADEClppldmS-KQPPTQELAAKDLHGNEWRFKHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--R 212 99***************************63.4445569********************************************..4 PP SSEE..EEEEE-S CS B3 87 rsefelvvkvfrk 99 +++el+v+v+r+ Vradi0185s00050.1 213 GENGELRVGVRRA 225 49999***996 PP
2	Auxin_resp	118.6	5.1e-39	250	332	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha+ t+++F+v+Y+Pr+s++eF+v++++++++lk+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp rW++SkWr+Lk Vradi0185s00050.1 250 AWHAILTGTIFTVYYKPRTSPAEFIVPYDQYMESLKNSYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDSDPNRWRESKWRCLK 332 79*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	9.68E-40	120	253	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	5.3E-41	121	239	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.01E-21	122	224	No hit	No description
Pfam	PF02362	1.3E-21	124	225	IPR003340	B3 DNA binding domain
SMART	SM01019	8.9E-23	124	226	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.843	124	226	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.8E-36	250	332	IPR010525	Auxin response factor
Pfam	PF02309	2.4E-12	684	784	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.592	696	778	IPR000270	PB1 domain
SuperFamily	SSF54277	1.37E-11	696	773	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009725	Biological Process	response to hormone
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 876 aa Download sequence Send to blast
MQHYDMATCV YKYLSYRDYA RSVADERSVV RSVEMASSEV TMKGNCLNHI DGGAVEAQAP 60 ATAKDAEAAL FRELWHACAG PLAEPDTDEV FAQVTLLPEP NQNENDVEKE PPPPPPPRFH 120 VHSFCKTLTA SDTSTHGGFS VLRRHADECL PPLDMSKQPP TQELAAKDLH GNEWRFKHIF 180 RGQPRRHLLQ SGWSVFVSSK RLVAGDAFIF LRGENGELRV GVRRAMRQQG NVPSSVISSH 240 SMHLGVLATA WHAILTGTIF TVYYKPRTSP AEFIVPYDQY MESLKNSYSI GMRFKMRFEG 300 EEAPEQRFTG TIVGIEDSDP NRWRESKWRC LKVRWDETSN TPRPERVSPW KIEPALAPPA 360 LNPLSMPRPK RPRSNAVPSS PDSSVLTREA ASSKVSVDPS PANGFPRVLQ GQEFSTLRGN 420 LGESNDSDAA EKSVVWPPAA VDDEKIDAST SRRYGTESWM SMGRNEPTYS DLLSSFGAGG 480 DLSHSSLMDQ MSPVVYPTRK QSADHEGKLH MPQPWPAMPS SLSLNILDSN TKGPAHGGDP 540 TYQARGNLRY SAFGEYPALH HKVEHSHGNL MPPPPAPLNQ YQTPCSREVM SKPVSTKTFE 600 AVKLKDGDCK LFGFSLISGP IVPEPSVPQR NVNEPTGQMH LTPHQQRTSE NDEKSDHSKG 660 SKTADDLTVD DHDRPLQTSQ LHAKDGQAKP LSSSARSCTK VHKKGIALGR SVDLTKYTGY 720 DELVAELDQL FEFEGELLST KKDWLIVYTD NEGDMMLVGD DPWQEFCTMV RKIYIYPKEE 780 IQKMSPGTLS SKNEENLSGS EGADAKDVKQ SGYERKPSSR MHHRQGQLAV SCANRVSALA 840 TILDSRISFH RELVDSQPKP FNFANFDVDA RFSFL*

Sequence ? help Back to Top

Protein Sequence Length: 876 aa Download sequence Send to blast

MQHYDMATCV YKYLSYRDYA RSVADERSVV RSVEMASSEV TMKGNCLNHI DGGAVEAQAP  60
ATAKDAEAAL FRELWHACAG PLAEPDTDEV FAQVTLLPEP NQNENDVEKE PPPPPPPRFH  120
VHSFCKTLTA SDTSTHGGFS VLRRHADECL PPLDMSKQPP TQELAAKDLH GNEWRFKHIF  180
RGQPRRHLLQ SGWSVFVSSK RLVAGDAFIF LRGENGELRV GVRRAMRQQG NVPSSVISSH  240
SMHLGVLATA WHAILTGTIF TVYYKPRTSP AEFIVPYDQY MESLKNSYSI GMRFKMRFEG  300
EEAPEQRFTG TIVGIEDSDP NRWRESKWRC LKVRWDETSN TPRPERVSPW KIEPALAPPA  360
LNPLSMPRPK RPRSNAVPSS PDSSVLTREA ASSKVSVDPS PANGFPRVLQ GQEFSTLRGN  420
LGESNDSDAA EKSVVWPPAA VDDEKIDAST SRRYGTESWM SMGRNEPTYS DLLSSFGAGG  480
DLSHSSLMDQ MSPVVYPTRK QSADHEGKLH MPQPWPAMPS SLSLNILDSN TKGPAHGGDP  540
TYQARGNLRY SAFGEYPALH HKVEHSHGNL MPPPPAPLNQ YQTPCSREVM SKPVSTKTFE  600
AVKLKDGDCK LFGFSLISGP IVPEPSVPQR NVNEPTGQMH LTPHQQRTSE NDEKSDHSKG  660
SKTADDLTVD DHDRPLQTSQ LHAKDGQAKP LSSSARSCTK VHKKGIALGR SVDLTKYTGY  720
DELVAELDQL FEFEGELLST KKDWLIVYTD NEGDMMLVGD DPWQEFCTMV RKIYIYPKEE  780
IQKMSPGTLS SKNEENLSGS EGADAKDVKQ SGYERKPSSR MHHRQGQLAV SCANRVSALA  840
TILDSRISFH RELVDSQPKP FNFANFDVDA RFSFL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-139	69	354	18	354	Auxin response factor 1
4ldw_A	1e-139	69	354	18	354	Auxin response factor 1
4ldw_B	1e-139	69	354	18	354	Auxin response factor 1
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Functional Description ? help Back to Top
Source	Description
UniProt	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs) (By similarity). Could act as transcriptional activator or repressor (PubMed:26959229, PubMed:26716451, PubMed:27645097, PubMed:28167023). Involved in the control of fruit ripening process (PubMed:26959229, PubMed:26716451, PubMed:28167023). Regulates expression of a number of ripening regulators, transcription factors, and ethylene biosynthesis and signaling components (PubMed:26959229, PubMed:26716451). May act as a transcriptional repressor of auxin-responsive genes (PubMed:26716451). Regulates vegetative growth, lateral root formation and flower organ senescence, possibly partially by regulating gene expression of auxin and ethylene response factor (ERF) genes (PubMed:28167023). Plays a negative role in axillary shoot meristem formation (PubMed:27645097). {ECO:0000255\|RuleBase:RU004561, ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Vradi0185s00050.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By tomato fruit ripening. Expression in tomato fruits is up-regulated by exogenous application of ethylene and down-regulated by inhibition of ethylene receptors with 1-methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-regulated by plant hormone abscisic acid (ABA) in tomato fruits (PubMed:26959229). Expression is not up-regulated by plant hormone auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin and gibberellic acid (GA), and down-regulated by ethylene in seedlings (PubMed:28167023). Down-regulated during decapitation-induced axillary shoot development and by excision of immature leaves. Down-regulation is inhibited by the application of auxin on the cut surface (PubMed:27645097). {ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AP015035	0.0	AP015035.1 Vigna angularis var. angularis DNA, chromosome 2, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_014522344.1	0.0	auxin response factor 2A isoform X1
Refseq	XP_022632057.1	0.0	auxin response factor 2A isoform X1
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	A0A1S3VWB3	0.0	A0A1S3VWB3_VIGRR; Auxin response factor
STRING	XP_007137862.1	0.0	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF3281	33	66

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G62000.3	0.0	auxin response factor 2

Publications ? help Back to Top
Tomato Genome Consortium The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 2012. 485(7400): p. 635-41 [PMID:22660326] Breitel DA, et al. AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening. PLoS Genet., 2016. 12(3): p. e1005903 [PMID:26959229] Xu T, et al. SlARF2a plays a negative role in mediating axillary shoot formation. Sci Rep, 2016. 6: p. 33728 [PMID:27645097] Ren Z,Liu R,Gu W,Dong X The Solanum lycopersicum auxin response factor SlARF2 participates in regulating lateral root formation and flower organ senescence. Plant Sci., 2017. 256: p. 103-111 [PMID:28167023]